Šulc Petr, Ouldridge Thomas E, Romano Flavio, Doye Jonathan P K, Louis Ard A
Center for Studies in Physics and Biology, Rockefeller University, New York, New York; Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom.
Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom; Department of Mathematics, Imperial College, London, United Kingdom.
Biophys J. 2015 Mar 10;108(5):1238-47. doi: 10.1016/j.bpj.2015.01.023.
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds.
我们使用最近开发的RNA粗粒度模型研究了RNA引发链介导的链置换反应的热力学和动力学。链置换是指一条单链取代先前与互补底物链结合的另一条链，这是活性核酸纳米技术中的一种基本机制，并且也被推测在体内会发生。我们研究了置换反应速率与引发链长度和温度的函数关系，并做出了两个可通过实验验证的预测：如果引发链位于底物的5'端，置换反应会更快；对于较长的引发链，置换反应会随着温度升高而减慢。
